diff --git a/cobra/__init__.py b/cobra/__init__.py index f2f548995..189574db0 100644 --- a/cobra/__init__.py +++ b/cobra/__init__.py @@ -13,7 +13,7 @@ DictList, Gene, Metabolite, Model, Object, Reaction, Species) from cobra.util.version_info import show_versions -__version__ = "0.7.0" +__version__ = "0.8.0" # set the warning format to be prettier and fit on one line _cobra_path = _dirname(_abspath(__file__)) diff --git a/release-notes/0.8.0.md b/release-notes/0.8.0.md new file mode 100644 index 000000000..a02141a2d --- /dev/null +++ b/release-notes/0.8.0.md @@ -0,0 +1,27 @@ +# Release notes for cobrapy 0.8.0 + +## Fixes + +- Tests no longer generates warnings about using deprecated functions. +- Gapfilling integrality thresholds now supported for all optlang solvers. + +## New features + +- `Model.slim_optimize()` can be used perform optimization without + creating a solution. Can lead to significant speedup compared to + `Model.optimize` when repeatedly doing optimizations and only making + use of the objective value as avoiding the need to fetch all values + from the solver object. +- solution, model, metabolite and reaction now have html + representation so they give more informative prints in jupyter + notebooks. +- New convenience functions `cobra.flux_analysis.find_essential_genes` and + `cobra.flux_analysis.find_essential_reactions`. +- `Model.optimize` has new parameter `raise_error` to enable option to + get trigger exception if no feasible solution could be found. +- `str(reaction)` now gives the more useful reaction id and the + reaction string. + +## Deprecated features + +- `str(reaction)` no longer gives `reaction.id`. diff --git a/release-notes/next-release.md b/release-notes/next-release.md index 2fdf80d70..c622d3598 100644 --- a/release-notes/next-release.md +++ b/release-notes/next-release.md @@ -4,21 +4,4 @@ ## New features -- `Model.slim_optimize()` can be used perform optimization without - creating a solution. Can lead to significant speedup compared to - `Model.optimize` when repeatedly doing optimizations and only making - use of the objective value as avoiding the need to fetch all values - from the solver object. -- solution, model, metabolite and reaction now have html - representation so they give more informative prints in jupyter - notebooks. -- New convenience functions `cobra.flux_analysis.find_essential_genes` and - `cobra.flux_analysis.find_essential_reactions`. -- `Model.optimize` has new parameter `raise_error` to enable option to - get trigger exception if no feasible solution could be found. -- `str(reaction)` now gives the more useful reaction id and the - reaction string. - ## Deprecated features - -- `str(reaction)` no longer gives `reaction.id`. diff --git a/setup.cfg b/setup.cfg index 6554b0b37..2a07966ee 100644 --- a/setup.cfg +++ b/setup.cfg @@ -1,5 +1,5 @@ [bumpversion] -current_version = 0.7.0 +current_version = 0.8.0 commit = True tag = True parse = (?P\d+) diff --git a/setup.py b/setup.py index 4f8c2f910..3ade6fd25 100644 --- a/setup.py +++ b/setup.py @@ -144,7 +144,7 @@ def build_extension(self, ext): setup( name="cobra", - version="0.7.0", + version="0.8.0", packages=find_packages(), setup_requires=setup_requirements, install_requires=["future", "swiglpk", "optlang>=1.2.1",